Contacts of the helix formed by residues 221 - 244 (chain A) in PDB entry 4ND1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ILE* 4.7 2.7 - - - -
218A GLY* 5.9 2.9 - - - +
220A ILE* 1.3 77.7 - - - +
222A GLN* 1.3 58.7 + - - +
223A GLU* 3.5 9.8 + - - +
224A GLN* 2.8 45.7 + - - +
225A ILE* 3.0 32.1 + - - +
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Residues in contact with GLN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A THR* 5.5 1.2 + - - -
216A ILE* 3.9 25.2 - - + +
221A THR* 1.3 74.1 - - - +
223A GLU* 1.3 57.6 + - + +
225A ILE* 3.3 22.0 + - - +
226A ASP* 2.7 66.6 + - - +
403A GOL 4.4 10.7 + - - -
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A THR* 3.2 9.5 + - - +
222A GLN* 1.3 76.2 - - + +
224A GLN* 1.3 58.8 + - + +
226A ASP* 3.2 12.7 + - - +
227A GLU* 2.8 28.9 + - - +
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Residues in contact with GLN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A HIS* 3.5 25.0 + - + +
219A LEU 4.6 0.3 - - - +
220A ILE* 3.4 17.5 - - + -
221A THR* 2.8 52.9 + - - +
223A GLU* 1.3 73.6 - - + +
225A ILE* 1.3 64.9 + - - +
227A GLU* 3.4 7.8 + - - +
228A ILE* 3.0 32.0 + - + +
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 6.1 0.7 - - + -
203A THR* 3.4 33.4 - - + -
212A LEU* 4.1 26.5 - - + -
216A ILE* 3.7 33.4 - - + -
220A ILE* 3.7 20.4 - - + -
221A THR 3.0 16.4 + - - +
222A GLN* 3.5 24.7 - - - +
223A GLU 3.3 0.2 - - - -
224A GLN* 1.3 75.5 - - - +
226A ASP* 1.3 59.5 + - - +
228A ILE* 3.3 10.6 + - + +
229A VAL* 2.9 27.4 + - + +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLN* 2.7 51.8 + - - +
223A GLU* 3.2 14.0 + - - +
225A ILE* 1.3 74.9 - - - +
227A GLU* 1.3 58.8 + - - +
229A VAL* 3.4 9.2 + - - +
230A CYS* 3.0 28.8 + - - +
403A GOL 4.5 7.1 + - - -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU 2.8 19.2 + - - +
224A GLN* 3.6 8.8 - - - +
225A ILE 3.4 0.2 - - - -
226A ASP* 1.3 73.1 - - - +
228A ILE* 1.3 69.1 + - - +
230A CYS* 3.4 6.1 + - + +
231A HIS* 2.8 45.4 + - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 3.9 24.5 - - + -
175A PHE* 3.8 38.9 - - + +
176A ILE* 4.0 17.7 - - + -
179A HIS* 4.3 10.3 - - + +
220A ILE* 4.2 21.8 - - + -
224A GLN* 3.0 20.4 + - + +
225A ILE* 3.5 10.3 - - + +
226A ASP 3.2 0.2 - - - -
227A GLU* 1.3 84.1 - - - +
229A VAL* 1.3 55.7 + - - +
231A HIS* 3.7 4.9 - - - +
232A THR* 2.7 37.8 + - - +
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 4.3 3.6 - - + -
201A PRO* 3.8 26.2 - - + +
203A THR* 3.5 29.2 - - + -
225A ILE* 2.9 21.6 + - + +
226A ASP* 3.7 9.0 - - - +
227A GLU 3.3 0.2 - - - -
228A ILE* 1.3 75.7 - - - +
230A CYS* 1.3 62.9 + - - +
232A THR* 3.4 4.8 + - - -
233A ARG* 3.1 35.1 + - - +
403A GOL 3.8 23.8 - - - +
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Residues in contact with CYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP 3.0 17.2 + - - +
227A GLU* 3.6 7.0 - - - +
229A VAL* 1.3 75.1 - - - +
231A HIS* 1.3 65.8 + - - +
233A ARG* 3.0 20.2 + - - +
234A ILE* 3.0 41.7 + - - +
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 3.3 44.4 - + + +
227A GLU* 2.8 39.8 + - - +
228A ILE* 3.7 6.5 - - - +
230A CYS* 1.3 73.8 - - - +
232A THR* 1.3 58.1 - - - +
234A ILE* 3.4 16.5 + - + -
235A ALA* 2.9 29.4 + - - +
238A GLU* 2.6 36.5 + - - -
64B LEU* 6.2 2.0 - - + -
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 3.6 26.2 - - - +
171A ARG* 4.7 5.6 + - + -
172A PHE* 3.4 33.0 - - + +
175A PHE* 3.7 12.7 - - - -
191A VAL* 4.0 11.4 - - + -
199A MET* 4.0 13.9 - - - +
201A PRO* 4.1 10.3 - - + -
228A ILE 2.7 23.2 + - - -
229A VAL 3.4 6.5 - - - -
230A CYS 3.3 0.2 - - - -
231A HIS* 1.3 77.9 - - - +
233A ARG* 1.3 61.6 + - - +
234A ILE 3.5 0.2 + - - -
235A ALA* 3.5 12.7 + - - +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG* 4.9 0.7 + - - -
196A GLY 4.6 3.3 - - - +
197A ASP* 2.9 44.8 + - - +
198A GLY* 4.8 2.8 - - - -
199A MET* 3.8 46.6 + - + +
201A PRO* 4.3 4.7 - - + -
229A VAL* 3.1 34.5 + - - +
230A CYS* 3.0 16.1 + - - +
232A THR* 1.3 77.2 - - - +
234A ILE* 1.3 69.9 + - + +
235A ALA 3.4 0.6 + - - -
236A TRP* 4.2 11.1 - - - -
314A LEU* 6.4 0.2 - - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP* 5.6 6.1 - - - +
230A CYS* 3.0 33.7 + - - +
231A HIS* 3.8 21.3 - - + +
233A ARG* 1.3 87.5 - - + +
235A ALA* 1.3 65.9 + - - +
236A TRP* 3.2 8.3 - - - +
237A LYS* 3.1 28.2 + - + +
238A GLU* 3.5 14.1 + - + +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG* 3.7 29.8 - - - +
175A PHE* 4.4 13.9 - - + -
231A HIS 2.9 17.0 + - - +
232A THR 3.5 11.9 - - - +
233A ARG 3.4 2.4 - - - -
234A ILE* 1.3 78.6 - - - +
236A TRP* 1.3 61.7 + - - +
238A GLU* 3.2 13.8 + - - +
239A VAL* 3.2 24.8 + - - +
68B HIS* 4.9 2.7 - - + -
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Residues in contact with TRP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.7 22.0 - - - -
105A PRO* 3.8 35.9 - - + -
107A ASP* 3.8 13.5 - - - -
108A ASP* 4.0 10.5 - - - -
109A ARG* 3.2 39.7 - - + +
171A ARG* 4.1 4.7 - - - +
197A ASP* 4.5 7.7 + - - -
233A ARG 4.2 12.8 + - - -
234A ILE* 3.1 4.0 + - - +
235A ALA* 1.3 78.3 - - - +
237A LYS* 1.3 94.1 + - + +
239A VAL* 3.6 3.4 + - - +
240A ALA* 3.0 28.8 + - - +
245A THR* 4.0 18.0 - - + +
246A ALA 5.3 1.6 + - - -
402A OXM 3.3 49.8 + - - +
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ARG* 5.2 3.6 - - - +
106A LYS 5.6 1.1 - - - +
107A ASP* 3.4 32.8 + - + +
197A ASP* 5.2 9.8 + - - -
234A ILE* 3.1 20.8 + - + +
236A TRP* 1.3 120.1 - - + +
238A GLU* 1.3 60.3 + - - +
240A ALA* 4.3 4.7 - - - -
241A ASP* 2.8 47.0 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PHE* 4.8 2.9 - - - -
231A HIS* 2.6 36.1 + - - -
234A ILE* 3.5 14.9 + - + +
235A ALA* 3.2 13.6 + - - +
237A LYS* 1.3 79.8 - - - +
239A VAL* 1.3 58.9 + - - +
241A ASP* 4.1 4.0 - - - +
242A ASN* 2.8 37.0 + - - +
64B LEU* 3.7 31.6 - - + +
68B HIS* 5.5 3.3 + - - -
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ARG* 4.6 7.0 - - - +
235A ALA 3.2 12.7 + - - +
236A TRP* 3.9 6.7 - - - +
238A GLU* 1.3 76.3 - - + +
240A ALA* 1.3 66.0 + - - +
242A ASN* 3.1 7.1 + - - +
243A LEU* 3.0 44.2 + - + +
246A ALA* 3.7 22.4 - - + -
61B GLY* 4.0 13.6 - - - +
64B LEU* 4.4 8.3 - - + -
65B ASP* 4.1 14.1 - - + +
68B HIS* 3.9 26.2 - - + +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.5 32.1 + - - +
236A TRP* 3.0 20.3 + - + +
237A LYS* 3.8 4.7 - - - +
239A VAL* 1.3 76.9 - - - +
241A ASP* 1.3 57.0 + - - +
244A GLY* 2.9 53.0 + - - -
245A THR* 4.0 14.8 - - + +
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Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.4 19.8 + - - +
237A LYS* 2.8 36.9 + - - +
238A GLU* 4.1 5.0 - - - +
240A ALA* 1.3 72.7 - - - +
242A ASN* 1.3 61.4 + - - +
244A LYS* 4.1 14.2 + - - +
57B GLY* 5.5 0.3 - - - -
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Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 2.8 27.9 + - - +
239A VAL 3.1 4.3 + - - +
241A ASP* 1.3 81.0 - - - +
243A LEU* 1.3 63.2 + - - +
244A LYS* 3.3 7.2 + - - +
57B GLY* 3.0 46.4 - - - +
58B ILE* 3.2 2.8 + - - -
60B GLN* 4.0 9.5 - - - +
61B GLY* 3.4 24.2 - - - -
64B LEU* 4.1 15.2 - - - +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A VAL* 3.0 38.4 + - + +
242A ASN* 1.3 73.3 - - - +
244A LYS* 1.3 93.9 + - + +
245A THR 3.5 28.3 - - - +
246A ALA* 4.3 0.2 - - - -
247A TYR* 4.0 19.7 - - + -
58B ILE* 3.1 22.6 - - + +
61B GLY* 3.8 2.9 - - - -
62B LYS* 3.7 46.9 - - + +
65B ASP* 4.7 2.0 - - - +
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Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 4.3 14.9 + - - +
240A ALA 2.9 14.9 + - - +
241A ASP* 4.1 10.6 + - - +
242A ASN 3.3 11.0 - - - +
243A LEU* 1.3 79.6 - - - +
244A THR* 1.3 68.6 + - - +
56B GLU* 3.8 42.0 + - - +
57B GLY* 5.6 0.2 - - - -
58B ILE* 4.5 8.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il